AMBER Archive (2008)

Subject: Re: AMBER: ptraj: new mask parser

From: Jianyin Shao (jyshao2004_at_gmail.com)
Date: Thu Jan 24 2008 - 11:23:53 CST

There might be bugs in ptraj, especially in the mask parser. :P
 But using the following command should get the heavy atoms you want:

":1-466_at_C*,N*,O*,P*"

Hope that helps.

Jianyin

On 1/23/08, Vlad Cojocaru <Vlad.Cojocaru_at_eml-r.villa-bosch.de> wrote:
>
> Dear amber users,
>
> I was trying tu use the following mask string in ptraj (the version
> distributed with AMBER 9)
>
> ":1-466 & !@H="
>
> to select the heavy atoms of a protein. According to the AMBER 9 manual
> this should work if enclosed in double quotes (which I did). However I
> always get an error saying "the = symbol wasnt recognized"
>
> The "=" symbol is described in the manual as an accepted mask wildcard
> in the new mask parser.
>
> Could somebody tell me why is this happening? Is there a bug that I am
> not aware of ?
>
> Thanks
>
> vlad
>
> --
>
> ----------------------------------------------------------------------------
> Dr. Vlad Cojocaru
>
> EML Research gGmbH
> Schloss-Wolfsbrunnenweg 33
> 69118 Heidelberg
>
> Tel: ++49-6221-533266
> Fax: ++49-6221-533298
>
> e-mail:Vlad.Cojocaru[at]eml-r.villa-bosch.de
>
> http://projects.villa-bosch.de/mcm/people/cojocaru/
>
>
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